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While developers at Microsoft Corp. may be celebrating that they finished work on Service Pack 2 (SP2) for Windows XP, IT departments around the world now face the question on whether they should update their systems, or not.

IBM Corp., for one, is holding off on installing the security focused update for Windows XP. In a note headlined “To patch — or not to patch” posted Friday on its corporate intranet, IBM tells its employees not to download SP2 when it becomes available because of compatibility issues. A copy of the note was obtained by IDG News Service.

“While this patch may be good news for other Microsoft Windows XP owners, IBM is directing XP users not to install SP2,” the note states. With close to 400,000 desktops, IBM is a very large Microsoft customer.

“IBM’s large number of Web applications will need to be tested and some modified to work correctly with SP2. Currently, some high profile, business-critical applications are also known to conflict with SP2,” IBM tells its employees in the note. “When the current issues and concerns have been addressed, IBM will deploy a customized version of SP2.”

An IBM spokesperson declined to comment on the company’s internal IT issues.

IBM alerted its users on the same day Microsoft started the process of delivering SP2 to end users by announcing release to manufacturing (RTM) of the service pack. The Windows XP update will be available soon through downloads, retail distribution and free CDs, as well as on new PCs. A network installation package will be available for enterprise users.

SP2 for Windows XP is more than the usual roll-up of bug fixes and updates. Microsoft has made something of a trade-off, focusing on security at the expense of compatibility. As a result, SP2 can render existing applications inoperable. Microsoft has urged developers and IT professionals to test the update.

Not only IBM is showing evidence of compatibility issues with XP SP2. Microsoft’s own software is also affected. Earlier this week the software vendor released an update for Microsoft CRM (Customer Relationship Management) 1.2 because SP2 will prevent the original application from running correctly.

Because of the broad changes, analysts have compared the XP service pack to a Windows upgrade instead of a simple update. Business users typically take much longer to install a new version of Windows than a service pack because of compatibility testing.

Thomas Smith, manager of desktop engineering at a large Houston-based company, hopes to be able to equip his 5,000 desktops with a customized version of the service pack before Microsoft pushes it out on Windows Update, he said.

Many of the desktops Smith manages are scattered throughout North America and connected using common high-speed Internet connections such as DSL or cable. While the company uses a remote management tool supplied by Altiris Inc., Smith said he relies on Windows Update for patching. If the standard Windows XP SP2 distribution is applied to his machines, it will block access to several corporate Web applications, Smith said.

Microsoft will help users in Smith’s position, said Barry Goffe, a group manager in Microsoft’s Windows group. The software maker plans to offer simple ways to set a unique registry key on XP desktops that will instruct the systems to skip Service Pack 2, but still download other critical updates through Windows Update and Automatic Update, Goffe said. “We want to give customers some breathing room,” he said.

Nevertheless, Microsoft urges all users to install SP2 as soon as they can, Goffe said.

“This is not about fun and games. SP2 is about improving the security of our customers’ infrastructure. We have spent a lot of time making sure that this delivers a lot of value to all our customers. We’re urging all customers to deploy SP2 as soon as possible,” he said.

Business users obviously need to test, but Microsoft can’t be blamed if users are now unpleasantly surprised by SP2, said Michael Cherry, a lead analyst at Directions on Microsoft Inc., in Kirkland, Wash.

“Microsoft has been more than forthcoming about the number of changes in this service pack and making it available for testing,” Cherry said. “I would say to IT departments that they want to get their testing done quickly because there are significant improvements in this service pack and I am not sure you would want to forego those.”

A first beta of Windows XP SP2 was released in December, followed by Release Candidate 1 in March and a second release candidate in June. Hundreds of thousands of developers and IT professionals have already tried out the software. The service pack represents one of Microsoft’s most broadly tested products to date, the company has said.